AttributeError: 'LayoutLine' object has no attribute 'sizes'

[Dengdengdeng-lab]

Hello, when I was using the software, I submitted the command: python -m jcvi.graphics.karyotype seqids layout. Then I encountered an error. The specific error information is as follows:

[04/22/25 19:16:07] DEBUG    Load file `layout`                       base.py:36
                    DEBUG    Load file `A.bed`                        base.py:36
[04/22/25 19:16:08] DEBUG    Load file `B.bed`                        base.py:36
Traceback (most recent call last):
  File "miniconda3/envs/jcvi_env/lib/python3.10/runpy.py", line 196, in _run_module_as_main
    return _run_code(code, main_globals, None,
  File /miniconda3/envs/jcvi_env/lib/python3.10/runpy.py", line 86, in _run_code
    exec(code, run_globals)
  File "envs/jcvi_env/lib/python3.10/site-packages/jcvi/graphics/karyotype.py", line XX, in <module>
    main(sys.argv[1:])
  File3/envs/jcvi_env/lib/python3.10/site-packages/jcvi/graphics/karyotype.py", line XX, in main
    Karyotype(
  File "miniconda3/envs/jcvi_env/lib/python3.10/site-packages/jcvi/graphics/karyotype.py", line XX, in __init__
    tr = Track(root, lo, gap=gap, height=height, lw=lw, draw=False)
  File "miniconda3/envs/jcvi_env/lib/python3.10/site-packages/jcvi/graphics/karyotype.py", line XX, in __init__
    self.sizes = sizes = t.sizes
AttributeError: 'LayoutLine' object has no attribute 'sizes'

I can't solve this problem on my own and I'm asking for help. Also, when I tried to generate the "sizes" file, I couldn't do it. The prompt said that I already had the file, but I actually don't have it. I would like to request your help. Thank you!

[GurjotSinghSidhu]

Can you upload your layout file as well? This will help to troubleshoot.

[Dengdengdeng-lab]

Thank you very much for your reply! Below is the content of my layout file. Could you please help me take a look:

# y, xstart, xend, rotation, color, label, va,  bed  
.6,     .2,    .8,       0,      , melon, top, A.bed  
.4,     .2,    .8,       0,      , melon1, top, B.bed  
# edges  
e,0,1,aly.ath.anchors.simple  

Thank you again for your reply!

[GurjotSinghSidhu]

I tested your layout file on my data and it worked fine, which seems to suggest that the problem lies in your upstream files (like A.bed, B.bed, or aly.ath.anchors.simple). I am not an expert but just trying to help!